[English] 日本語
Yorodumi
- PDB-1kp5: Cyclic Green Fluorescent Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kp5
TitleCyclic Green Fluorescent Protein
ComponentsGreen Fluorescent Protein
KeywordsLUMINESCENT PROTEIN / cyclised termini / cyclic protein / green fluorescent protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Green fluorescent protein
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHofmann, A. / Iwai, H. / Plueckthun, A. / Wlodawer, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structure of cyclized green fluorescent protein.
Authors: Hofmann, A. / Iwai, H. / Hess, S. / Pluckthun, A. / Wlodawer, A.
History
DepositionDec 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 21, 2015Group: Structure summary
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id
Remark 999sequence the difference between the sequence database and the coordinates is that GYS 76 represents ...sequence the difference between the sequence database and the coordinates is that GYS 76 represents the chromophore (ser-tyr-gly). also, the residue numbering is not sequential - numbers 75 and 77 are skipped in the coordinates.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green Fluorescent Protein
B: Green Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,70310
Polymers55,9352
Non-polymers7698
Water1,69394
1
A: Green Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3525
Polymers27,9671
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Green Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3525
Polymers27,9671
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Green Fluorescent Protein
hetero molecules

A: Green Fluorescent Protein
hetero molecules

B: Green Fluorescent Protein
hetero molecules

B: Green Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,40620
Polymers111,8694
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
crystal symmetry operation5_555y,-x+y,z+1/61
crystal symmetry operation8_665x-y+1,-y+1,-z1
Buried area10530 Å2
ΔGint-239 kcal/mol
Surface area35980 Å2
MethodPISA
4
A: Green Fluorescent Protein
B: Green Fluorescent Protein
hetero molecules

A: Green Fluorescent Protein
B: Green Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,40620
Polymers111,8694
Non-polymers1,53716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area6930 Å2
ΔGint-229 kcal/mol
Surface area39580 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-108 kcal/mol
Surface area20340 Å2
MethodPISA
6
B: Green Fluorescent Protein
hetero molecules

A: Green Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,70310
Polymers55,9352
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_565x-y,-y+1,-z1
Buried area2130 Å2
ΔGint-106 kcal/mol
Surface area21120 Å2
MethodPISA
7
A: Green Fluorescent Protein
hetero molecules

A: Green Fluorescent Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,70310
Polymers55,9352
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2420 Å2
ΔGint-104 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.447, 142.447, 183.809
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein Green Fluorescent Protein /


Mass: 27967.369 Da / Num. of mol.: 2
Mutation: M1S,S2R,Q25H,Q80R,F99S,Y100F,M141L,M153T,P157Q,V163A,K172E,I219V,I229L,T230V,H231P,G232R,M233G,D234T,E235G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish) / Production host: Escherichia coli (E. coli) / References: UniProt: P42212
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.81 Å3/Da / Density % sol: 74.43 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 10
Details: ammonium sulfate, glycine, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
pH: 10
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.1 Mammonium sulfate1reservoir
20.1 Mglycine1reservoirpH10.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. all: 31910 / Num. obs: 31910 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 26
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 6 / Num. unique all: 3340 / % possible all: 99.3
Reflection
*PLUS
Lowest resolution: 25 Å / Num. obs: 34481 / Num. measured all: 917968 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.503

-
Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1emm

1emm


Resolution: 2.6→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 187412.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3193 10 %RANDOM
Rwork0.208 ---
all-31869 --
obs-31869 92.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.7304 Å2 / ksol: 0.356122 e/Å3
Displacement parametersBiso mean: 38.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.73 Å23.6 Å20 Å2
2---7.73 Å20 Å2
3---15.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 40 94 3936
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it2.823
X-RAY DIFFRACTIONc_mcangle_it4.223.5
X-RAY DIFFRACTIONc_scbond_it4.323.5
X-RAY DIFFRACTIONc_scangle_it5.864
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 499 10.1 %
Rwork0.258 4465 -
obs-4964 88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CRO.PARCRO.TOP
X-RAY DIFFRACTION5CYCL.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.256 / Rfactor Rwork: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.319 / Rfactor Rwork: 0.258

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more